In February of 2152 Phlox was assigned to decontaminate the quarters of Crewman Daniels, who had been revealed to be a time-traveler from the 31st century. While in Daniels' quarters, Phlox discovered a device that allowed him to travel through time at will. He decided to use the device to time travel to 2124 and rescue Xesophia, then the love of his life, before the accident in which she drowned. He speculated that if she had lived he would have married her.

The device didn't work as Phlox hoped, and he was only able to travel back ten months, shortly after Enterprise's launch. With Daniels' assistance, Phlox was able to use the device to return to the proper time, but not before glimpsing a possible future in which Enterprise was under attack by Nausicaanpirates. (ENTshort story: "Cabin E-14")

By 2165 his daughter Vaneel had fallen in love with the AntaranPehle Retab, and the couple married in mid 2165. The wedding was marred when Pehle's father Sohon Retab was murdered by Phlox's son Mettus. The murder of the elder Retab - a popular figure among the Antaran people - caused considerable tension between the Denobulan and Antaran people. The Denobulan government was considering extraditing Mettus when he was kidnapped by the True Sons of Antar, an extremist group that wanted to conduct a show trial followed by an execution.

Phlox traveled to Antar where he convinced their Central Investigation Bureau to mount a raid to stop the True Sons. Phlox saved the life of Mettus by taking a shot from the True Sons leader that was meant for him. Phlox soon recovered from his injuries and visited his son in the Antaran prison where he was being held. In that clean and relatively comfortable facility, Mettus had a great deal of time to think about what he had done. The two men finally came to terms with Mettus' crime, and with each other. (ENT - Rise of the Federationnovel: Live by the Code)

Phlox's influence was felt in the 2380s when a virus similar to the Epsilon Zeta VII one affected the Space Station Diamandis 1 . A Starfleet team's consultations with Admiral Leonard McCoy revealed the story behind the Epsilon Zeta infection and Phlox's assistance in resolving that situation, leading to the resolution of the Diamandis situation. (STcomic: "Flesh and Stone")